if not args.prefix:
prefix = ""
else:
prefix = args.prefix + "-"
outfilename = prefix + "cnvs.csv"
# Prep the output file.
with open(outfilename, "w") as outfile:
MQ.runTime("# CNV VCF parsing", outfile)
MQ.PWS("# VCF File: " + args.input, outfile)
MQ.PWS("# Samples File: " + args.samples, outfile)
MQ.PWS("# Output prefix: " + args.prefix, outfile)
MQ.PWS("# Output file: " + outfilename, outfile)
MQ.PWS("# ----------", outfile)
MQ.PWS("# " + MQ.getDateTime() + " Reading sample info...", outfile)
samples = cnvlib.readSamples(args.samples)
MQ.PWS("# " + MQ.getDateTime() + " Samples read: " + str(len(samples)),
outfile)
# Read the sample info.
MQ.PWS("# " + MQ.getDateTime() + " Reading VCF...", outfile)
vcf, vcf_headers, vcf_format, human_flag = cnvlib.readVCF(args.input)
MQ.PWS("# " + MQ.getDateTime() + " Variants read: " + str(len(vcf)),
outfile)
# Read the VCF file.
MQ.PWS("# " + MQ.getDateTime() + " Fixing VCF headers...", outfile)
vcf_headers = [h.replace("NHP-", "") for h in vcf_headers]
if "39239A" in vcf_headers:
vcf_headers[vcf_headers.index("39239A")] = "39239"
MQ.PWS("# Gene file: " + gene_file, logfile)
MQ.PWS("# 10kb up file: " + gene_up_file, logfile)
MQ.PWS("# 10kb down file: " + gene_down_file, logfile)
MQ.PWS("# Transcript file: " + transcript_file, logfile)
MQ.PWS("# Exon file: " + exon_file, logfile)
MQ.PWS("# ----------------", logfile)
# I/O options and info.
feature_types = [
"gene", "gene-10kb-up", "gene-10kb-down", "transcript", "exon"
]
cnv_types = ["del", "dup"]
overlap_types = ["full", "partial"]
# Categories for features, CNVs, and overlaps.
MQ.PWS("# " + MQ.getDateTime() + " Reading CNVs...", logfile)
cnvs = []
for line in open(cnvs_file):
cnv = line.strip().split("\t")[3]
cnv_len = int(cnv.split(":")[3])
if cnv_len < max_cnv_len:
cnvs.append(cnv)
num_cnvs = len(cnvs)
MQ.PWS("# CNVs read: " + str(num_cnvs), logfile)
MQ.PWS("\n# " + MQ.getDateTime() + " Counting gene overlaps...", logfile)
countOverlaps(cnvs, gene_file, "GENES")
MQ.PWS(
"\n# " + MQ.getDateTime() + " Counting 10kb upstream gene overlaps...",
logfile)
MQ.runTime("# Fisher's test for GO enrichment", outfile)
MQ.PWS(MQ.spacedOut("# Query file:", io_pad) + queryfile, outfile)
MQ.PWS(MQ.spacedOut("# Background file:", io_pad) + bgfile, outfile)
MQ.PWS(
MQ.spacedOut("# Alpha (p-value threshold):", io_pad) + str(alpha),
outfile)
MQ.PWS(
MQ.spacedOut("# Multiple test correction method:", io_pad) +
correction_str, outfile)
if correction == "None":
MQ.PWS("# --> WARNING: Not correcting for multiple tests!", outfile)
MQ.PWS(MQ.spacedOut("# Output file:", io_pad) + outfilename, outfile)
MQ.PWS("# ----------", outfile)
# Report I/O information.
MQ.PWS("# " + MQ.getDateTime() + " Counting total query GO terms...",
outfile)
query_genes = []
query_go_count = 0
for line in open(queryfile):
if line[0] == "#":
continue
line = line.strip().split("\t")
gid = line[0]
if gid not in query_genes:
query_genes.append(gid)
query_go_count += 1
# Get count of query GO terms and unique list of features.
MQ.PWS("# " + MQ.getDateTime() + " Counting total background GO terms...",
outfile)
gofile = "go/" + species + "-go-terms-uniq.txt"
transcripts_file = "go/" + species + "-noalu-transcripts-" + mode + ".txt"
# The input files: A GO term database from Ensembl (with identical lines removed with bash's sort | uniq commands)
# and a file containing transcript IDs that overlap CNVs (from 06_gene_count_bed.py)
queryoutfile = "go/" + species + "-cnv-" + mode + "-go-query.tab"
bgoutfile = "go/" + species + "-cnv-" + mode + "-go-bg.tab"
MQ.PWS("# Go file : " + gofile)
MQ.PWS("# Transcripts file : " + transcripts_file)
MQ.PWS("# Mode : " + mode)
MQ.PWS("# Query out : " + queryoutfile)
MQ.PWS("# BG out : " + bgoutfile)
MQ.PWS("# ----------------")
MQ.PWS("# " + MQ.getDateTime() + " Getting annotation info...")
transcript_go = {}
go_accs = {}
first = True
for line in gzip.open(gofile):
if first:
first = False
continue
line = line.decode().strip().split("\t")
#print(line);
chrome = line[4]
if chrome == "MT":
continue
dumpfile = "../cafe-data/dump.out.mlemur-blast.txt.I30"
overlap_file = "bed/" + species + "-cnvs-filtered-noalu.csv"
gtf_file = "gtf/" + species + "-chromes.gtf"
overlap_file = "bed/" + species + "-cnvs-to-transcripts.bed"
outfilename = "../cafe-data/" + species + "-cafe-genes" + ".csv"
# File names.
MQ.PWS("# Log file: " + logfilename, logfile)
MQ.PWS("# GTF file: " + gtf_file, logfile)
MQ.PWS("# Overlap file:" + overlap_file, logfile)
MQ.PWS("# Dump file: " + dumpfile, logfile)
MQ.PWS("# Output file: " + outfilename, logfile)
MQ.PWS("# ----------------", logfile)
# I/O options and info.
MQ.PWS("# " + MQ.getDateTime() + " Reading features from GTF...", logfile)
ttp = defaultdict(str)
overlaps = {}
for line in open(gtf_file):
if line[0] == "#":
continue
line = line.strip().split("\t")
feature_type, chrome, start, end, feature_info = line[2], line[0], int(
line[3]), int(line[4]), line[8]
if feature_type == "CDS":
tid = re.findall('ENS' + regstr + 'T[\d]+', feature_info)[0]
pid = re.findall('ENS' + regstr + 'P[\d]+', feature_info)[0]
if pid not in ttp[tid]:
ttp[tid] = pid
overlaps[tid] = {